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Clusters were linked using the Ward's linkage rule that minimizes intra-cluster variance.
Therefore, no linkage rule is required in seriation in addition to the distance metric used to define similarities.
Trees were re-sampled by jackknifing with 1,000 iterations with Pearson correlation as the distance matric and complete linkage rule.
Due to this fact, following clustering analysis of gene expression datasets, all genes are assigned to the most appropriate cluster based on a generic linkage rule.
In contrast, following seriation analysis that does not require a linkage rule, contigs of genes with high pairwise correlation coefficients are revealed by reordering.
iTreg- and Teff-specific probes identified at different time points were hierarchically clustered based on their expression signals in iTregs and Teffs at the respective time point applying a Euclidean similarity measure and Complete linkage rule.
Similar(31)
Another advantage of the approach is that it bypasses the problem of choosing linkage rules and dissimilarity measures, the choice of which cannot always be traced back to theoretical economic criteria.
We will only consider inversion-free linkage rules here.
Hierarchical cluster diagrams were built using a Pearson centered distance measure under average linkage rules.
After standardizing the data, cluster analysis was performed using squared Euclidean distances and Ward's method linkage rules (Ward 1963).
Unsupervised hierarchical clustering using average linkage rules and a Pearson centered distance metric was performed to assess the overall degree of gene expression similarity among samples [ 18].
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